ArticleGenome biology2012
Novel origins of copy number variation in the dog genome.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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54 citing papers in PubMed, 88 citations in OpenAlex.
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- Towards the detection of copy number variation from single sperm sequencing in cattle.BMC genomics · 2022Article
- Copy number variation underlies complex phenotypes in domestic dog breeds and other canids.Genome research · 2021Article
- A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.Communications biology · 2021Article
- A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing.BMC genomics · 2021Article
- Analysis of Structural Variants Reveal Novel Selective Regions in the Genome of Meishan Pigs by Whole Genome Sequencing.Frontiers in genetics · 2021Article
- Whole genome resequencing of the Iranian native dogs and wolves to unravel variome during dog domestication.BMC genomics · 2020Article
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- Population structure and genetic history of Tibetan Terriers.Genetics, selection, evolution : GSE · 2019Article
- Genome-wide detection of copy number variations in polled yak using the Illumina BovineHD BeadChip.BMC genomics · 2019Article
- A Genome-Wide Detection of Copy Number Variations Using SNP Genotyping Arrays in Braque Français Type Pyrénées Dogs.Animals : an open access journal from MDPI · 2019Article
- Probe-based association analysis identifies several deletions associated with average daily gain in beef cattle.BMC genomics · 2019Article
- Copy number variation study in Japanese quail associated with stress related traits using whole genome re-sequencing data.PloS one · 2019Article
- A Survey of Copy Number Variation in the Porcine Genome Detected From Whole-Genome Sequence.Frontiers in genetics · 2019Article
- Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle.Frontiers in genetics · 2019Article
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Authors and funding
12 authors at 7 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCopy number variants (CNVs) account for substantial variation between genomes and are a major source of normal and pathogenic phenotypic differences. The dog is an ideal model to investigate mutational mechanisms that generate CNVs as its genome lacks a functional ortholog of the PRDM9 gene implicated in recombination and CNV formation in humans. Here we comprehensively assay CNVs using high-density array comparative genomic hybridization in 50 dogs from 17 dog breeds and 3 gray wolves.
resultsWe use a stringent new method to identify a total of 430 high-confidence CNV loci, which range in size from 9 kb to 1.6 Mb and span 26.4 Mb, or 1.08%, of the assayed dog genome, overlapping 413 annotated genes. Of CNVs observed in each breed, 98% are also observed in multiple breeds. CNVs predicted to disrupt gene function are significantly less common than expected by chance. We identify a significant overrepresentation of peaks of GC content, previously shown to be enriched in dog recombination hotspots, in the vicinity of CNV breakpoints.
conclusionsA number of the CNVs identified by this study are candidates for generating breed-specific phenotypes. Purifying selection seems to be a major factor shaping structural variation in the dog genome, suggesting that many CNVs are deleterious. Localized peaks of GC content appear to be novel sites of CNV formation in the dog genome by non-allelic homologous recombination, potentially activated by the loss of PRDM9. These sequence features may have driven genome instability and chromosomal rearrangements throughout canid evolution.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.